Experiment set2IT079 for Bifidobacterium breve UCC2003

CDM1 without Nicotinate

Group: nutrient dropout
Media: CDM1 + no Nicotinate, pH=7
Culturing: Bifido_ML2, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Anthony Shiver on 12/10/2019
Growth plate: CDM1_nutrientdrop G7

Specific Phenotypes

For 3 genes in this experiment

For nutrient dropout no Nicotinate in Bifidobacterium breve UCC2003

For nutrient dropout no Nicotinate across organisms

SEED Subsystems

Subsystem	#Specific
NAD and NADP cofactor biosynthesis global	2
NAD regulation	2
Acetoin, butanediol metabolism	1
Branched-Chain Amino Acid Biosynthesis	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine biosynthesis
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Nicotinate and nicotinamide metabolism
• Pantothenate and CoA biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyruvate fermentation to (R)-acetoin II	2	2	1
NAD de novo biosynthesis I	6	6	2
NAD de novo biosynthesis III	6	5	2
NAD de novo biosynthesis IV (anaerobic)	6	5	2
pyruvate fermentation to (S)-acetoin	3	2	1
pyruvate fermentation to (R)-acetoin I	3	2	1
L-valine biosynthesis	4	4	1
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde	4	4	1
nicotine biosynthesis	9	3	2
pyruvate fermentation to isobutanol (engineered)	5	4	1
superpathway of (R,R)-butanediol biosynthesis	5	3	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of nicotine biosynthesis	12	4	2
superpathway of 2,3-butanediol biosynthesis	6	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	6	1
superpathway of branched chain amino acid biosynthesis	17	17	2
NAD de novo biosynthesis II (from tryptophan)	9	4	1
aspartate superpathway	25	23	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of NAD biosynthesis in eukaryotes	14	6	1
superpathway of L-threonine metabolism	18	13	1